LAMMPS (18 Jul 2015)
# 250 butane system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.butane
  orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  5 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  4250 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6750 dihedrals
  5 = max # of 1-2 neighbors
  8 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  17 = max # of special neighbors

group gBUTANE molecule 1:250
4500 atoms in group gBUTANE
group gCORES type 1 2 3
3500 atoms in group gCORES
group gDRUDES type 4 5
1000 atoms in group gDRUDES

pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff    1    * thole 1.368000
pair_coeff    2    * thole 1.368000
pair_coeff    4    * thole 1.368000
pair_coeff    5    * thole 1.368000

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C N D D

fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
  0 = # of size 2 clusters
  500 = # of size 3 clusters
  500 = # of size 4 clusters
  0 = # of frozen angles

comm_modify vel yes
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  G vector (1/distance) = 0.367867
  grid = 36 36 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031354
  estimated relative force accuracy = 9.44215e-05
  using double precision FFTs
  3d grid and FFT values/proc = 79507 46656
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 17
New max number of 1-2 to 1-4 neighbors: 17 (+0)
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 10
  ghost atom cutoff = 10
Memory usage per processor = 20.1567 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] 
       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    -353319.1    55742.797    334.61375    18.435655 
      50    2.8816051    2130.0808    1490.8248    136.43926    639.25601    192.16834    670.26518    115.15685            0    -766.5636    595300.83    -594872.6    2829.5958    55742.797    187.32686   0.60253137 
     100     5.569447    2172.0554    1656.5476    151.60609    515.50773    180.41449    708.03397    165.80788            0   -971.62525    595305.35   -594872.47     1231.388    55742.797    208.34096   0.16151117 
     150    8.2248161     2216.471    1733.4485      158.644    483.02256    136.16281    713.34485    169.62608            0   -964.30363    595300.47   -594872.27    4400.6234    55742.797    218.02975   0.12336382 
     200    10.911476    2271.1314    1750.9955     160.2499    520.13587    190.12953    725.63606    167.04635            0   -987.11203     595295.5   -594871.06    2107.4949    55742.797    220.19714   0.23035017 
     250    13.588019    2333.7822    1793.0252    164.09642    540.75705    153.18169    833.95287     168.1507            0   -1041.2955     595297.2   -594870.43    1165.6922    55742.797    225.18334    1.0339004 
     300     16.26521    2403.6147    1909.3441    174.74185    494.27059    144.27299     803.8452    155.85505            0   -1036.4615    595297.31   -594870.55    2511.3721    55742.797    239.06243    3.0455686 
     350    18.937858    2448.2389      1862.67    170.47027    585.56885    181.70523     821.7917    164.10713            0   -1005.4167     595293.5   -594870.12    2874.0826    55742.797    233.92745    1.0806435 
     400    21.590191    2498.6994    1942.5496     177.7808    556.14976     168.5792    828.99117     182.0756            0    -1050.149    595296.43   -594869.77    485.86761    55742.797    244.23632    0.3882729 
     450    24.247025    2552.9641    1890.0917    172.97989    662.87241    134.42613     957.3361    181.42951            0   -1036.4237    595295.53   -594869.43    66.452669    55742.797    237.65323   0.34464588 
     500    26.850275      2608.55    1970.0729    180.29971     638.4771    187.01392    838.62129    176.10775            0   -985.23355    595290.89   -594868.93    3471.1633    55742.797    247.59402   0.66791252 
     550    29.482354     2667.002    1875.8227    171.67399    791.17931    178.48765    1003.6885    176.78989            0   -991.21705    595292.35   -594868.92    1767.0543    55742.797    235.34039    1.7252619 
     600     32.10773    2715.2399     1883.279    172.35639    831.96094    186.79504    1047.6877    183.04311            0   -1010.5423    595293.27   -594868.29    931.85523    55742.797    236.28437    1.7094253 
     650    34.715398    2754.4497     1970.794     180.3657    783.65568    166.02823    963.09399     184.8464            0   -952.45217    595290.25   -594868.11     2640.017    55742.797    247.67755   0.68709275 
     700    37.337317    2795.9461    1928.2674     176.4737    867.67874    176.09641    1002.4636    186.11483            0   -920.14356    595291.32   -594868.18    664.78904    55742.797    242.41897   0.44316381 
     750    39.927419    2838.2052    2043.2258    186.99461    794.97945    170.34991    941.73148    193.53082            0   -940.49604     595298.1   -594868.23    410.24758    55742.797    256.84035   0.55229077 
     800    42.469991    2881.9788    1945.9722    178.09402    936.00667     197.5203    1021.5571    202.83524            0   -915.18511    595297.49   -594868.21   -716.81442    55742.797    244.35112    1.2303511 
     850     45.05362    2923.3858    2106.5752    192.79231    816.81052    195.94987    886.41681    184.36064            0   -878.10485    595296.29    -594868.1   -1407.5711    55742.797     264.3276    1.8387296 
     900    47.651245    2950.6673    2039.6221     186.6648    911.04515    183.79618    1000.7954    184.49766            0   -890.38965    595299.97   -594867.63    -1085.794    55742.797    256.21167    1.0198208 
     950    50.451391    2976.6436    2006.5932    183.64202    970.05039    228.60059    985.21322    206.18529            0   -881.65815    595299.54   -594867.83   -1851.9703    55742.797    252.23637   0.54012241 
    1000    53.018937     3003.743    2056.8471    188.24122    946.89587    171.73287    976.85675    207.05097            0   -836.24563    595294.95   -594867.45    282.61914    55742.797     258.5658   0.52076804 
    1050    55.532595    3031.3535    2095.4846     191.7773    935.86887    203.54188    945.75569     204.8504            0   -846.10969    595294.45   -594866.62   -376.91112    55742.797    263.27093   0.93584407 
    1100    58.115412    3058.5347    2047.3098    187.36838    1011.2249    211.94076     1001.093    223.66214            0   -855.82424    595297.13   -594866.78   -1381.6531    55742.797    256.93409    1.6724456 
    1150    60.799698    3078.3996    2123.1811    194.31206    955.21855    189.50189    937.18685    224.21465            0   -823.63222    595294.38   -594866.43    524.70113    55742.797     266.5974    1.3568376 
    1200    63.295243     3093.556    2005.8939    183.57802    1087.6621     201.3428    1044.9909    219.39202            0   -805.37122    595293.83   -594866.52   -370.32492    55742.797     252.0829   0.71475597 
    1250    65.797931    3108.5155    2175.8972    199.13661    932.61826     156.6571    969.72254    225.30586            0   -850.00503    595297.25   -594866.31   -1015.3093    55742.797    273.53154   0.55100418 
    1300    68.300441    3122.9792    2090.3719    191.30939    1032.6073    209.92015    984.36624    236.75408            0   -825.27583    595292.92   -594866.08   -798.51816    55742.797    262.69421   0.75855207 
    1350    70.793202    3136.8213      2084.47    190.76925    1052.3513    186.49827    1004.7564    234.55362            0   -798.08335    595290.25   -594865.63    702.53782    55742.797    261.71553    1.3884089 
    1400    73.326733    3144.9028    2180.3659    199.54558    964.53687    170.02484    962.43948    235.07761            0   -829.27156    595291.77   -594865.51    1682.2488    55742.797     273.7286    1.5246324 
    1450    75.821906    3146.3365    2013.3816    184.26329    1132.9549    193.77936    1084.1403     252.3227            0   -821.23045    595288.54    -594864.6   -160.21484    55742.797    252.96375   0.87780357 
    1500    78.325264    3150.6861    2107.4863    192.87569    1043.1998    185.11752    988.72532    245.47682            0   -796.86739    595285.46   -594864.71    2242.3101    55742.797    264.90216   0.61222547 
    1550    80.779931    3156.3483    2074.5953    189.86552    1081.7531    166.52863    1062.4971    238.93518            0   -810.65247    595289.34    -594864.9    2224.9015    55742.797    260.73559   0.68881715 
    1600    83.275807    3163.8714    2000.6756    183.10045    1163.1958    210.70823    1110.4519    256.16493            0    -840.1463    595290.73   -594864.71   -830.17884    55742.797    251.26533    1.1443116 
    1650    85.768304    3169.3489    2056.4309    188.20313     1112.918     214.6419     1021.762    268.00157            0   -815.69477       595289    -594864.8    813.12089    55742.797    258.12835    1.5476743 
    1700    88.261463    3168.7666    2119.4079    193.96675    1049.3587    147.25006    1027.6415    246.49221            0   -797.55007    595290.74   -594865.22    412.59618    55742.797    266.23017    1.0703149 
    1750    90.746918    3168.2304    2066.7675    189.14913     1101.463    224.44009    1005.0052    243.56874            0   -797.83359    595291.25   -594864.96   -858.91314    55742.797    259.74684   0.69942293 
    1800    93.246077    3169.7579    2109.6017    193.06929    1060.1562    204.57678    981.05867    249.37843            0   -801.42006    595291.51   -594864.95    137.05559    55742.797    265.15197   0.65571606 
    1850    95.734661    3174.8532    2133.5052    195.25692     1041.348    175.87566    982.18775    244.55231            0   -786.49546    595290.43   -594865.21    882.03323    55742.797    268.02768     1.006296 
    1900    98.221874    3180.3842    2106.4808    192.78367    1073.9034     207.8879    977.47746    250.68948            0   -788.04039    595290.55   -594864.66    574.40162    55742.797    264.45175    1.4759897 
    1950    100.72148     3182.921    2084.8893    190.80763    1098.0317    207.26976    1007.5583    256.52302            0   -800.37789    595291.76   -594864.71   -981.75066    55742.797    261.81202     1.271779 
    2000    103.20588    3185.2881    2079.8136     190.3431    1105.4745    185.44441    1008.6997     251.0561            0   -766.97142    595292.22   -594864.97    661.65951    55742.797    261.35563   0.78600155 
Loop time of 103.206 on 1 procs for 2000 steps with 4500 atoms

Pair  time (%) = 60.3651 (58.49)
Bond  time (%) = 16.8315 (16.3087)
Kspce time (%) = 20.1106 (19.4859)
Neigh time (%) = 1.52801 (1.48054)
Comm  time (%) = 0.328804 (0.318591)
Outpt time (%) = 0.00495553 (0.00480159)
Other time (%) = 4.03695 (3.91155)

Nlocal:    4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    10060 ave 10060 max 10060 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    774908 ave 774908 max 774908 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 774908
Ave neighs/atom = 172.202
Ave special neighs/atom = 13.3333
Neighbor list builds = 35
Dangerous builds = 0
